IPI - International Protein Index

1. effectively maintains a database of cross references between the primary data sources
2. provides minimally redundant yet maximally complete sets of proteins for featured species (one sequence per transcript)
3. maintains stable identifiers (with incremental versioning) to allow the tracking of sequences in IPI between IPI releases.

ANNOUNCEMENT: IPI Closure

IPI was launched in 2001 when there was a great deal of uncertainty about the correct human gene count, and many contradictions between different databases. Since then, the situation has improved for many of the most-studied genomes. The CCDS project, a collaboration between Ensembl, NCBI and UCSC has resulted in a standard set of gene predictions for the human genome; although there is not yet agreement on every gene model, a common set of curated gene models now exist for most human genes. In addition, a further collaboration between Ensembl and UniProtKB has plugged the gaps that previously existed in the coverage of the human genome in the UniProt Knowlegebase; we have also incorporated the Arabdiposis data from TAIR previously missing in UniProt. Missing predictions from mouse and rat are scheduled for inclusion in the UniProtKB in the middle of March 2010.

We therefore are announcing that IPI will be closed later in 2010. We recommend the use of the UniProtKB as the protein database for use in mass spectrometry and other experiments. We will continue to make releases of IPI until at least four months after the inclusion of rat and mouse data in UniProt, and are continuing to work on ways to enhance the usefulness of this resource for mass spectrometry. If you would like more advice about the changes, please contact us.